fix migrations

tracex_project/extraction/logic/modules/module_cohort_tagger.py

@@ -68,7 +68,7 @@ def __remove_placeholder(cohort_data) -> Optional[Dict[str, str]]:
         return cohort_dict
 
     @staticmethod
-    def normalize_coniditons_snomed(cohort_dict):
+    def normalize_coniditons_snomed(cohort_dict) -> Optional[Dict[str, str]]:
         """Normalizes conditions to a SNOMED code."""
         condition = cohort_dict.get("condition")
         preexisting_condition = cohort_dict.get("preexisting_condition")

tracex_project/extraction/logic/orchestrator.py

@@ -266,17 +266,6 @@ def set_default_values(self) -> None:
             data["activity_relevance"] = None
             data["timestamp_correctness"] = None
             data["correctness_confidence"] = None
-        if "cohort_tagging" not in config_modules:
-            cohort_default_values = {
-                "age": None,
-                "gender": None,
-                "origin": None,
-                "condition": None,
-                "condition_snomed_code": None,
-                "preexisting_condition": None,
-                "preexisting_condition_snomed_code": None,
-            }
-            self.set_cohort(cohort_default_values)
 
     def update_progress(self, view, execution_step: int, module_name: str) -> None:
         """Update the progress of the extraction."""

tracex_project/extraction/migrations/0022_remove_cohort_gender_add_snomed_trace_cohort.py

@@ -0,0 +1,53 @@
+# Generated by Django 4.2.13 on 2024-05-26 09:35
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('extraction', '0021_alter_event_event_type_alter_event_location_and_more'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='trace',
+            name='cohort',
+        ),
+        migrations.AddField(
+            model_name='cohort',
+            name='condition_snomed_code',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='cohort',
+            name='preexisting_condition_snomed_code',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='cohort',
+            name='trace',
+            field=models.OneToOneField(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='cohort', to='extraction.trace'),
+        ),
+        migrations.AlterField(
+            model_name='cohort',
+            name='age',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name='cohort',
+            name='condition',
+            field=models.CharField(blank=True, max_length=50, null=True),
+        ),
+        migrations.AlterField(
+            model_name='cohort',
+            name='origin',
+            field=models.CharField(blank=True, max_length=50, null=True),
+        ),
+        migrations.AlterField(
+            model_name='cohort',
+            name='preexisting_condition',
+            field=models.CharField(blank=True, max_length=100, null=True),
+        ),
+    ]

tracex_project/extraction/migrations/0023_remove_cohort_gender_cohort_sex.py

@@ -0,0 +1,22 @@
+# Generated by Django 4.2.13 on 2024-05-26 09:41
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('extraction', '0022_remove_cohort_gender_add_snomed_trace_cohort'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='cohort',
+            name='gender',
+        ),
+        migrations.AddField(
+            model_name='cohort',
+            name='sex',
+            field=models.CharField(blank=True, max_length=25, null=True),
+        ),
+    ]